# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--THP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--THP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--THP2/seqs-shuffled # positives: 1073 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--THP2/seqs-centered (Sat Jan 18 21:08:25 PST 2020) # negatives: 1073 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--THP2/seqs-shuffled (Sat Jan 18 21:08:25 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 21:24:57 PST 2020 MEME version 4.12.0 ALPHABET "DNA" DNA-LIKE A "Adenine" CC0000 ~ T "Thymine" 008000 C "Cytosine" 0000CC ~ G "Guanine" FFB300 N "Any base" = ACGT X = ACGT . = ACGT V "Not T" = ACG H "Not G" = ACT D "Not C" = AGT B "Not A" = CGT M "Amino" = AC R "Purine" = AG W "Weak" = AT S "Strong" = CG Y "Pyrimidine" = CT K "Keto" = GT U = T END ALPHABET strands: + - Background letter frequencies (from dataset): A 0.298 C 0.200 G 0.200 T 0.301 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 107 18 9.6e-018 3.6e-013 # GGTTCGA TCGAACC 82 12 8.6e-015 3.2e-010 # GGATCGA TCGATCC 27 4 1.5e-005 5.6e-001 # GGCTCGA TCGAGCC 17 3 1.2e-003 4.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 107 E= 3.6e-013 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.233645 0.102804 0.000000 0.663551 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 59 4 3.4e-014 1.3e-009 # CTCGGCCA TGGCCGAG 28 2 3.7e-007 1.4e-002 # CTTGGCCA TGGCCAAG 20 1 9.7e-006 3.6e-001 # CTGGGCCA TGGCCCAG 11 1 3.1e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 1.3e-009 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.474576 0.186441 0.338983 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCCWTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GCCWTA TAWGGC 137 46 6.5e-013 2.4e-008 # GCCTTA TAAGGC 94 27 1.2e-010 4.4e-006 # GCCATA TATGGC 47 22 1.5e-003 5.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 147 E= 2.4e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.340136 0.000000 0.000000 0.659864 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TACCAYTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TACCAYTA TARTGGTA 38 0 2.6e-012 9.6e-008 # TACCACTA TAGTGGTA 28 0 3.1e-009 1.1e-004 # TACCATTA TAATGGTA 10 0 9.6e-004 3.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 9.6e-008 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.736842 0.000000 0.263158 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCRTAC GTAYGG 109 34 2.9e-011 1.1e-006 # CCATAC GTATGG 74 21 1.1e-008 4.0e-004 # CCGTAC GTACGG 40 14 2.3e-004 8.4e+000 letter-probability matrix: alength= 4 w= 6 nsites= 124 E= 1.1e-006 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.645161 0.000000 0.354839 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAGAAV DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAGAAV BTTCTT 413 276 1.5e-010 5.3e-006 # AAGAAA TTTCTT 247 158 5.6e-007 2.0e-002 # AAGAAG CTTCTT 138 88 2.7e-004 1.0e+001 # AAGAAC GTTCTT 92 59 3.4e-003 1.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 527 E= 5.3e-006 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.508539 0.187856 0.303605 0.000000 MOTIF GCTACYGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCTACYGA TCRGTAGC 32 0 1.8e-010 6.7e-006 # GCTACCGA TCGGTAGC 25 0 2.6e-008 9.3e-004 # GCTACTGA TCAGTAGC 7 0 7.7e-003 2.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 6.7e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.781250 0.000000 0.218750 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCANC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACCANC GNTGGT 247 143 3.4e-009 1.2e-004 # ACCATC GATGGT 78 40 2.1e-004 7.5e+000 # ACCACC GGTGGT 75 40 5.2e-004 1.9e+001 # ACCAGC GCTGGT 54 27 1.5e-003 5.4e+001 # ACCAAC GTTGGT 78 47 2.8e-003 9.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 291 E= 1.2e-004 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.268041 0.264605 0.195876 0.271478 0.000000 1.000000 0.000000 0.000000 MOTIF CCATCGTK DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCATCGTK MACGATGG 27 1 9.3e-008 3.3e-003 # CCATCGTT AACGATGG 17 1 6.8e-005 2.4e+000 # CCATCGTG CACGATGG 10 0 9.6e-004 3.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.3e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.370370 0.629630 MOTIF ACCGTGS DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACCGTGS SCACGGT 26 1 1.8e-007 6.4e-003 # ACCGTGC GCACGGT 12 0 2.4e-004 8.4e+000 # ACCGTGG CCACGGT 14 1 4.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 6.4e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.461538 0.538462 0.000000 MOTIF GGCGCTY DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GGCGCTY RAGCGCC 30 3 5.9e-007 2.1e-002 # GGCGCTT AAGCGCC 19 3 4.0e-004 1.4e+001 # GGCGCTC GAGCGCC 11 0 4.8e-004 1.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.1e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.366667 0.000000 0.633333 MOTIF CTGYTGC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CTGYTGC GCARCAG 37 6 6.5e-007 2.3e-002 # CTGCTGC GCAGCAG 19 3 4.0e-004 1.4e+001 # CTGTTGC GCAACAG 18 3 7.1e-004 2.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 2.3e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTTCAYC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTTCAYC GRTGAAG 50 13 1.1e-006 3.9e-002 # CTTCATC GATGAAG 32 8 8.0e-005 2.8e+000 # CTTCACC GGTGAAG 19 5 3.2e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 3.9e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.358491 0.000000 0.641509 0.000000 1.000000 0.000000 0.000000 MOTIF ATAGTRTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATAGTRTA TAYACTAT 26 2 1.3e-006 4.7e-002 # ATAGTGTA TACACTAT 19 2 1.0e-004 3.7e+000 # ATAGTATA TATACTAT 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.7e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.269231 0.000000 0.730769 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACTTKCG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CACTTKCG CGMAAGTG 23 1 1.3e-006 4.7e-002 # CACTTTCG CGAAAGTG 13 0 1.2e-004 4.2e+000 # CACTTGCG CGCAAGTG 10 1 5.8e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.7e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.434783 0.565217 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 103.51 seconds